Updates

Model and report changes

  1. We have extended the use of serological sampling data to use samples taken beyond the first wave of the pandemic. The samples are those collected by NHS Blood and Transplant using the Roche-N assay, which measures the prevalence of infection-acquired antibodies in the population.
  2. The model now accounts for the ongoing immunisation programme, stratifying the population of people still susceptible to infection with the virus according to their immunisation status (unimmunised/1 dose/2 doses). We use data on the daily proportions of the population getting immunised to inform this splitting of the population, assuming that it takes three weeks for vaccine-derived immunity to develop. Vaccine efficacy is assumed against both infection and death, using values for the efficacy in agreement with those found here. We have a changepoint in the vaccine efficacy on the 10th May, which marks a transition from alpha being the dominant variant, to delta.
  3. The model also accounts for a different susceptibility to infection in each adult age group (no prior information is used); and for the under-15s, (using prior information from Viner et al, 2020, which estimates children to be less likely to acquire infection when in contact with an infectious individual).
  4. The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly since the outset of the Survey in May 2020 for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths.
  5. The underlying probability of an unvaccinated individual dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) is allowed to change gradually over the course of 30 days every (approximately) 100 days. This is designed to reflect fluctuations due to seasonal effects, demand on healthcare services or the emergence of new virus variants of differing severity.
  6. The ‘Epidemic summary’ only reports the current value for the IFR by age. To visualise how this has changed over time in our model, see the IFR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of dying if infected, taking into account the impact of the immunisation programme - it is an average of a lower rate of death in vaccinated individuals and a higher rate among the unvaccinated.

Updated findings

  1. The estimated number of new daily infections on the 19th November across England is 41,300 (35,900–47,800, 95% credible interval). The daily infection rate is estimated to be 74 per 100k population per day nationally. The highest rate continues to be in the East Midlands (EM) with 122 infections per 100K population, corresponding to 5,840 daily infections respectively. These are followed by the rates in the East of England (EE), the West Midlands (WM) and the South East (SE) which are 91, 86 and 82 infections per 100k respectively. The North East (NE) has 78 daily infections per 100k, the South West (SW) and London (GL) have equal rates at 66 and Yorkshiregit and Humberside (YH) has 55 infections per 100k. The North West (NW) continues to have the lowest infection rates at 26 infections per 100k. Note that a substantial proportion of these infections will be asymptomatic.
  2. The daily number of deaths is now estimated to be declining, and we forecast between 78 and 133 deaths per day by the 10th of December, consistently with last week’s results.
  3. This week it is unlikely that Rt is bigger than 1 in any region, with no recovery in the values of Rt following the school half-term holiday.. There is a 23% chance that Rt>1 in EM and an 18% chance in SE, but everywhere else this chance is 9% or less.
  4. The growth rate for England remains at -0.01 (-0.01– -0.02) per day. This means that, nationally, the number of infections is decreasing, corresponding to an Rt of around 0.93, only slightly higher than last week.
  5. Our estimates for the attack rate, that is the proportion of the regional populations who have ever been infected, have NE at 59% and GL at 57%. WM, YH and NW are all also above the national average with 54%, 50% and 50% respectively.The SE and SW continue to have the lowest attack rates at 37% and 36%. These correspond to a very slight downward revision to last week.
  6. Note that the deaths data used are only very weakly informative on Rt over the last two weeks. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to some revision.

Interpretation

Our estimates show a pandemic with Rt values that are estimated to remain below 1. We can now be confident that this fall in transmission has now percolated through to the deaths, and we estimate the number of deaths occurring daily to have peaked in the first week of November at 154 deaths per day, much lower than the peaks of the first two waves of infection.

Plots of the IFR over time show that from the end of January we estimate a decreasing IFR in all adult age groups, but most steeply in the older ages. This drop indicates the benefits of immunisation against death over and above the benefits against infection. Following this drop, there has been a period of plateau followed by a gradual increase in the overall IFR to 0.27% (0.27%–0.28%). However, the age-specific IFRs appear to be falling, suggesting that the overall increase is due to shifting age patterns towards older people being infected. The estimated IFR is highest in the over-75s at 3.3% (3.1%–3.5%)

For context, in addition to the data used here, the number of reported new positive cases (by date of specimen) is clearly increasing. This increase, which would be expected following the national half-term holiday, will become concerning if it persists into the next week. As a caveat to this, trends in the number of reported cases are highly dependent on the volume and targeting of testing, the public’s testing behaviour and significant reporting delays, and therefore are difficult to interpret. Overall, there have been 8.5million positive tests, which, compared to our estimate of cumulative incidence, would suggest that, overall, around 1 in 3 infections have been identified. This seems plausible, particularly when considering the low ascertainment rates of the first wave. Like the deaths, hospitalisation admissions are steadily decreasing, and the prevalence of infection, as estimated by the ONS Coronavirus Infection Survey, has also decreased markedly, falling to 1.5% in England.

Summary

Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.

Methods

We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.

Data sources

We use:

  1. Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing This consists of a combination of deaths notified to:
    • the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
    • NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
    • Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020)
  2. Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors.

Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).

  1. Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
  2. Information on contacts between different age groups from:
    • A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
    • Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
    • The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
    • Data from the Department for Education describing the proportion of children currently attending school.
  3. Daily data on the numbers of people getting immunised by age-group and region. These data are derived from the National Immunisation Management Service (NIMS). These data includes all COVID-19 immunisations administered at hospital hubs, local immunisation service sites such as GP practices, and dedicated immunisation centres.

Epidemic summary

Current \(R_t\)

Value of \(R_t\), the average number of secondary infections due to a typical infection today.

Number of infections

Attack rate

The percentage of a given group that has been infected.

By region

By age

Current IFR

Change in infections incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England -0.01 -0.02 -0.01
East of England -0.01 -0.03 0.00
East Midlands -0.01 -0.03 0.01
London -0.01 -0.03 0.01
North East -0.02 -0.04 0.00
North West -0.04 -0.07 -0.02
South East -0.01 -0.03 0.01
South West -0.04 -0.06 -0.02
West Midlands -0.02 -0.04 0.00
Yorkshire and The Humber -0.03 -0.05 -0.01

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 46.64 32.10 83.28
East of England 46.86 21.93 NA
East Midlands 87.43 27.32 NA
London 64.37 24.01 NA
North East 33.69 15.50 NA
North West 16.46 10.04 40.88
South East 99.72 26.10 NA
South West 19.11 11.96 41.36
West Midlands 34.23 19.01 203.21
Yorkshire and The Humber 19.74 12.44 49.64

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA NA NA
East of England NA 919.57 NA
East Midlands NA 77.43 NA
London NA 121.16 NA
North East NA 551.71 NA
North West NA NA NA
South East NA 82.53 NA
South West NA NA NA
West Midlands NA NA NA
Yorkshire and The Humber NA NA NA

Change in deaths incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England -0.01 -0.01 -0.01
East of England -0.01 -0.02 0.01
East Midlands 0.00 -0.01 0.02
London -0.01 -0.02 0.01
North East -0.01 -0.02 0.01
North West -0.03 -0.04 -0.02
South East -0.01 -0.02 0.01
South West -0.02 -0.03 -0.01
West Midlands -0.01 -0.02 0.01
Yorkshire and The Humber -0.02 -0.03 -0.01

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 66.06 46.97 118.32
East of England 135.40 38.24 NA
East Midlands NA 61.33 NA
London 96.11 35.16 NA
North East 81.73 29.77 NA
North West 23.87 17.51 45.53
South East 99.95 35.31 NA
South West 32.96 21.73 78.69
West Midlands 74.18 33.38 NA
Yorkshire and The Humber 34.81 22.29 112.62

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA NA NA
East of England NA 74.90 NA
East Midlands 418.94 40.89 NA
London NA 114.01 NA
North East NA 94.34 NA
North West NA NA NA
South East NA 115.74 NA
South West NA NA NA
West Midlands NA 135.18 NA
Yorkshire and The Humber NA NA NA 
## The execution of the prevalence code block will proceed if
##  prev.dat exists and this is TRUE 
##  it is not and external report and this is FALSE

Infections and deaths

The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (19 Nov).

Infection incidence

By region

By age

Cumulative infections

By region

By age

Deaths incidence

By region

By age

Cumulative deaths

By region

By age

IFR

Prob \(R_t > 1\)

The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.

\(R_t\)

Copyright © MRC Biostatistics Unit, University of Cambridge